The vacuolar H +-ATPase (V-H +-ATPase) plays a crucial role in plant salt tolerance by energizing Na + sequestration into vacuoles and maintaining cytoplasmic Na +/K + homeostasis. Lycium barbarum L. ( L. barbarum) is a well-known halophytic plant. However, the mechanism by which he regulates ion balance to withstand salt stress is not very clear. In this study, we investigated the physiological and molecular mechanisms underlying V-H +-ATPase-mediated salt tolerance in L. barbarum. Under salt stress, L. barbarum exhibited dynamic changes in PM-H +-ATPase and V-H +-ATPase activities, with an initial increase followed by a decline under prolonged stress, correlating with altered Na + and K + distribution. Transcriptomic analysis revealed differential expression of V-H +-ATPase subunits, with the E subunit upregulated and others (A, B, C, H, a, c, d, e) downregulated, suggesting a fine-tuned regulatory response to salinity. Weighted gene co-expression network analysis (WGCNA) identified key modules and hub genes associated with K + homeostasis, highlighting their role in salt adaptation. Furthermore, transgenic overexpression of LbVHA-d2 and LbVHA-a3 in Nicotiana benthamiana ( N. benthamiana) enhanced salt tolerance by modulating H +-ATPase activity and improving Na +/K + balance, particularly in roots under prolonged stress. While LbVHA-d2 and LbVHA-a3 did not physically interact using yeast two-hybrid (Y2H), their co-expression influenced stress responses, indicating potential indirect regulatory crosstalk. Subcellular localization confirmed their plasma membrane association, supporting their role in proton gradient-driven ion transport. These findings demonstrate that V-H +-ATPase subunits critically regulate salt tolerance and provide potential genetic targets for improving crop resilience in saline environments.